My little ones STILL poop as they run. I sometimes wonder if it just kinda plops out without them noticing. Rabbits are a creature of habbit (if you wake up every day at 6am and give them a treat, after a while they will wake up when you do, or be up, and be bouncing around waiting for their treat!) so try putting the litter box where they are going. Use something a little heavier that will keep their box down so it cant be thrown. I use a kitten littler box so the walls are low enough that they can jump in, but high enough and large enough that they wont accidentally pee over the box. I use all natural bedding pellets in their potty box as it absorbs the smell and the liquid, and is heavier then their little teeth can lift! Also clean up the area where they have been peeing with a non-toxic odor killer.
If Zipper does begin going where you put the box, then you can leave it there if its not in the way, or just slowly begin to move it. Mine was, quite literally in the walkway, so, every time after they had both pottied, I would move it over just an inch or so. Due to the smell of their pee no longer being in the carpet, they just slowly began following the box until finally I was able to put it by the fire place (dont worry, we have it blocked off and never use it)